Background: In France, updated data on food allergies (FAs) are lacking, despite the need for efficient FA management and prevention. This study aimed to evaluate the prevalence of FAs in children in France, describe the most common allergens and determine the prevalence of atopic diseases in children with FAs. Methods: The ELFE study comprises a French nationwide birth cohort, including 18,329 children born in 2011. FAs were assessed by parental reports of food avoidance based on medical advice related to FAs, provided at 2 months and 2, 3.5 and 5.5 years of age. Data regarding FAs were available for 16,400 children. Data were weighted to account for selection and attrition bias. Results: From birth to 5.5 years of age, FAs were reported for 5.94% (95% CI: 5.54–6.34) children. Milk was the most common allergen, followed by egg, peanut, exotic fruits, tree nuts, gluten and fish. Among children with FAs, 20.5% had an allergy to at least two different groups of allergens; 71% reported eczema at least once before 5.5 years of age; 24.4% reported incidence of asthma; and 42.3% reported incidence of allergic rhinitis or conjunctivitis. Conclusion: In France, the prevalence of FAs in children up to 5.5 years of age is approximately 6%. It was demonstrated that 1 in 5 children with allergies had multiple FAs.